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Next-generation sequencing

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https://www.readbyqxmd.com/read/27922076/identification-of-bnayucca6-as-a-candidate-gene-for-branch-angle-in-brassica-napus-by-qtl-seq
#1
Hui Wang, Hongtao Cheng, Wenxiang Wang, Jia Liu, Mengyu Hao, Desheng Mei, Rijin Zhou, Li Fu, Qiong Hu
Oilseed rape (Brassica napus L.) is one of the most important oil crops in China as well as worldwide. Branch angle as a plant architecture component trait plays an important role for high density planting and yield performance. In this study, bulked segregant analysis (BSA) combined with next generation sequencing technology was used to fine map QTL for branch angle. A major QTL, designated as branch angle 1 (ba1) was identified on A06 and further validated by Indel marker-based classical QTL mapping in an F2 population...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922044/from-tumour-heterogeneity-to-advances-in-precision-treatment-of-colorectal-cancer
#2
REVIEW
Cornelis J A Punt, Miriam Koopman, Louis Vermeulen
In recent years, the high heterogeneity of colorectal cancer (CRC) has become evident. Hence, biomarkers need to be developed that enable the stratification of patients with CRC into different prognostic subgroups and in relation to response to therapies, according to the distinctive tumour biology. Currently, only RAS-mutation status is used routinely as a negative predictive marker to avoid treatment with anti-EGFR agents in patients with metastatic CRC, and mismatch-repair status can guide the use of adjuvant chemotherapy in patients with early stage colon cancer...
December 6, 2016: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/27921404/genome-wide-profiling-of-genetic-variation-in-agrobacterium-transformed-rice-plants
#3
Wen-Xu Li, San-Ling Wu, Yan-Hua Liu, Gu-Lei Jin, Hai-Jun Zhao, Long-Jiang Fan, Qing-Yao Shu
Agrobacterium-mediated transformation has been widely used in producing transgenic plants, and was recently used to generate "transgene-clean" targeted genomic modifications coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system. Although tremendous variation in morphological and agronomic traits, such as plant height, seed fertility, and grain size, was observed in transgenic plants, the underlying mechanisms are not yet well understood, and the types and frequency of genetic variation in transformed plants have not been fully disclosed...
2016: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/27921234/simultaneous-virus-identification-and-characterization-of-severe-unexplained-pneumonia-cases-using-a-metagenomics-sequencing-technique
#4
Xiaohui Zou, Guangpeng Tang, Xiang Zhao, Yan Huang, Tao Chen, Mingyu Lei, Wenbing Chen, Lei Yang, Wenfei Zhu, Li Zhuang, Jing Yang, Zhaomin Feng, Dayan Wang, Dingming Wang, Yuelong Shu
Many viruses can cause respiratory diseases in humans. Although great advances have been achieved in methods of diagnosis, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province, China. A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS. An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples...
December 2, 2016: Science China. Life Sciences
https://www.readbyqxmd.com/read/27921039/clinical-manifestation-and-management-of-adpkd-in-western-countries
#5
REVIEW
Claudia Sommerer, Martin Zeier
BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disease in Western countries. The prevalence is between 2.4/10,000 and 3.9/10,000. ADPKD represents a systemic disease resulting in deterioration in renal function. Until now, mutations in two genes (PKD1 and PKD2) have been identified. Recently, the European Medicines Agency (EMA) approved the use of the vasopressin V2 receptor antagonist tolvaptan to slow the progression of cyst development and renal insufficiency connected with ADPKD in adult patients with chronic kidney disease stages 1-3 at initiation of treatment with evidence of rapidly progressing disease...
October 2016: Kidney Diseases
https://www.readbyqxmd.com/read/27921038/the-clinical-manifestation-and-management-of-autosomal-dominant-polycystic-kidney-disease-in-china
#6
REVIEW
Cheng Xue, Chen-Chen Zhou, Ming Wu, Chang-Lin Mei
BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic hereditary kidney disease characterized by progressive enlargement of renal cysts. The incidence is 1-2‰ worldwide. Mutations in two genes (PKD1 and PKD2) cause ADPKD. Currently, there is no pharmaceutical treatment available for ADPKD patients in China. Summary: This review focused on advances in clinical manifestation, gene diagnosis, risk factors, and management of ADPKD in China. There is an age-dependent increase in total kidney volume (TKV) and decrease in renal function in Chinese ADPKD patients...
October 2016: Kidney Diseases
https://www.readbyqxmd.com/read/27920649/hepatoid-carcinoma-of-the-pancreas-case-report-next-generation-tumor-profiling-and-literature-review
#7
James M Chang, Nitin N Katariya, Dora M Lam-Himlin, Danielle J Haakinson, Ramesh K Ramanathan, Thorvardur R Halfdanarson, Mitesh J Borad, Rahul Pannala, Douglas Faigel, Adyr A Moss, Amit K Mathur
Fewer than 25 cases of hepatoid carcinoma of the pancreas have been reported in the literature. We present a case in a 61-year-old male with a remote history of Hodgkin's lymphoma and gastric neuroendocrine cell hyperplasia. On surveillance endoscopic ultrasound, an 8 × 5 mm cystic lesion was seen in the tail of the pancreas. MRI showed a focal pancreatic duct cut-off with mild ductal dilation. Fine needle aspiration was performed, which was concerning for acinar cell carcinoma. The patient underwent distal pancreatectomy and recovered uneventfully...
September 2016: Case Reports in Gastroenterology
https://www.readbyqxmd.com/read/27920633/lesch-nyhan-syndrome-models-theories-and-therapies
#8
REVIEW
Scott Bell, Ilaria Kolobova, Liam Crapper, Carl Ernst
Lesch-Nyhan syndrome (LNS) is a rare X-linked disorder caused by mutations in HPRT1, an important enzyme in the purine salvage pathway. Symptoms of LNS include dystonia, gout, intellectual disability, and self-mutilation. Despite having been characterized over 50 years ago, it remains unclear precisely how deficits in hypoxanthine and guanine recycling can lead to such a profound neurological phenotype. Several studies have proposed different hypotheses regarding the etiology of this disease, and several treatments have been tried in patients, though none have led to a satisfactory explanation of the disease...
November 2016: Molecular Syndromology
https://www.readbyqxmd.com/read/27920554/next-generation-sequence-detects-arap3-as-a-novel-oncogene-in-papillary-thyroid-carcinoma
#9
Qing-Xuan Wang, En-Dong Chen, Ye-Feng Cai, Yi-Li Zhou, Zhou-Ci Zheng, Ying-Hao Wang, Yi-Xiang Jin, Wen-Xu Jin, Xiao-Hua Zhang, Ou-Chen Wang
PURPOSE: Thyroid cancer is the most frequent malignancies of the endocrine system, and it has became the fastest growing type of cancer worldwide. Much still remains unknown about the molecular mechanisms of thyroid cancer. Studies have found that some certain relationship between ARAP3 and human cancer. However, the role of ARAP3 in thyroid cancer has not been well explained. This study aimed to investigate the role of ARAP3 gene in papillary thyroid carcinoma. METHODS: Whole exon sequence and whole genome sequence of primary papillary thyroid carcinoma (PTC) samples and matched adjacent normal thyroid tissue samples were performed and then bioinformatics analysis was carried out...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27919910/ph-like-acute-lymphoblastic-leukemia-a-high-risk-subtype-in-adults
#10
Nitin Jain, Kathryn G Roberts, Elias Jabbour, Keyur Patel, Agda Karina Eterovic, Ken Chen, Patrick Zweidler-McKay, Xinyan Lu, Gloria Fawcett, Sa A Wang, Sergej Konoplev, Richard C Harvey, I-Ming Chen, Debbie Payne-Turner, Marcus Valentine, Deborah Thomas, Guillermo Garcia-Manero, Farhad Ravandi, Jorge Cortes, Steven Kornblau, Susan O'Brien, Sherry Pierce, Jeffrey Jorgensen, Kenna R Mills Shaw, Cheryl L Willman, Charles G Mullighan, Hagop Kantarjian, Marina Konopleva
Ph-like acute lymphoblastic leukemia (ALL) is a high-risk subtype of ALL in children. There are limited and conflicted data on the incidence and prognosis of Ph-like ALL in adults. Patients with newly-diagnosed B-ALL who received frontline chemotherapy at MD Anderson Cancer Center underwent gene expression profiling of leukemic cells to identify Ph-like ALL. Patients received hyper-CVAD (80%) or augmented-BFM (20%) regimen. Of 148 patients, 33.1% had Ph-like, 31.1% had Ph+, and 35.8% had other B-ALL subtypes (B-other)...
December 5, 2016: Blood
https://www.readbyqxmd.com/read/27919631/effect-of-seasonal-vaccination-on-the-selection-of-influenza-a-h3n2-epidemic-variants
#11
Yong Chong, Hideyuki Ikematsu
The effect of vaccination on the dynamics of influenza virus variants remains largely unknown in humans, unlike in poultry. In this study, we compared influenza hemagglutinin (HA) gene sequences isolated from vaccinated and unvaccinated populations with the yearly vaccine strains. In total, 181 influenza A/H3N2 virus samples isolated from 82 vaccinated and 99 unvaccinated patients (2011-15, four Japanese influenza seasons) were genetically analyzed using a next-generation sequencer. Amino acid (AA) differences from corresponding vaccine strains were found in 74 of 329 HA1 sites...
December 2, 2016: Vaccine
https://www.readbyqxmd.com/read/27918649/big-data-from-small-samples-informatics-of-next-generation-sequencing-in-cytopathology
#12
REVIEW
Sinchita Roy-Chowdhuri, Somak Roy, Sara E Monaco, Mark J Routbort, Liron Pantanowitz
The rapid adoption of next-generation sequencing (NGS) in clinical molecular laboratories has redefined the practice of cytopathology. Instead of simply being used as a diagnostic tool, cytopathology has evolved into a practice providing important genomic information that guides clinical management. The recent emphasis on maximizing limited-volume cytology samples for ancillary molecular studies, including NGS, requires cytopathologists not only to be more involved in specimen collection and processing techniques but also to be aware of downstream testing and informatics issues...
December 5, 2016: Cancer
https://www.readbyqxmd.com/read/27918560/genome-wide-chemical-mapping-of-o-glcnacylated-proteins-in-drosophila-melanogaster
#13
Ta-Wei Liu, Mike Myschyshyn, Donald A Sinclair, Samy Cecioni, Kevin Beja, Barry M Honda, Ryan D Morin, David J Vocadlo
N-Acetylglucosamine β-O-linked to nucleocytoplasmic proteins (O-GlcNAc) is implicated in the regulation of gene expression in organisms, from humans to Drosophila melanogaster. Within Drosophila, O-GlcNAc transferase (OGT) is one of the Polycomb group proteins (PcGs) that act through Polycomb group response elements (PREs) to silence homeotic (HOX) and other PcG target genes. Using Drosophila, we identify new O-GlcNAcylated PcG proteins and develop an antibody-free metabolic feeding approach to chemoselectively map genomic loci enriched in O-GlcNAc using next-generation sequencing...
December 5, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27918477/identification-and-characterisation-of-the-antimicrobial-peptide-phylloseptin-pt-from-the-skin-secretion-of-phyllomedusa-tarsius-and-comparison-of-activity-with-designed-cationicity-enhanced-analogues-and-diastereomers
#14
Yitian Gao, Di Wu, Xinping Xi, Yue Wu, Chengbang Ma, Mei Zhou, Lei Wang, Mu Yang, Tianbao Chen, Chris Shaw
Antimicrobial peptides belonging to the phylloseptin family are mainly found in phyllomedusine frogs. These peptides not only possess potent antimicrobial activity but exhibit low toxicity against eukaryotic cells. Therefore, they are considered as promising drug candidates for a number of diseases. In a recent study, potent antimicrobial activity was correlated with the conserved structures and cationic amphiphilic characteristics of members of this peptide family. A phylloseptin peptide precursor was discovered here in the skin secretion of Phyllomedusa tarsius and the mature peptide was validated by MS/MS sequencing, and was subsequently named phylloseptin-PT...
December 3, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27918106/cannabidiol-activates-neuronal-precursor-genes-in-human-gingival-mesenchymal-stromal-cells
#15
Thangavelu Soundara Rajan, Sabrina Giacoppo, Domenico Scionti, Francesca Diomede, Gianpaolo Grassi, Federica Pollastro, Adriano Piattelli, Placido Bramanti, Emanuela Mazzon, Oriana Trubiani
In the last years, mesenchymal stromal cells (MSCs) from oral tissues have received considerable interest in regenerative medicine since they can be obtained with minimal invasive procedure and exhibit immunomodulatory properties. This study was aimed to investigate whether in vitro pre-treatment of MSCs obtained from human gingiva (hGMSCs) with Cannabidiol (CBD), a cannabinoid component produced by the plant Cannabis sativa, may promote human gingiva derived MSCs to differentiate towards neuronal precursor cells...
December 5, 2016: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/27917594/a-novel-two-nucleotide-deletion-in-hps6-affects-mepacrine-uptake-and-platelet-dense-granule-secretion-in-a-family-with-hermansky-pudlak-syndrome
#16
Oliver Andres, Verena Wiegering, Eva-Maria König, Anna Lena Schneider, Daniela Semeniak, Simon Stritt, Eva Klopocki, Harald Schulze
BACKGROUND: Hermansky-Pudlak syndrome (HPS) is a rare autosomal recessive disease characterized by oculocutaneous albinism and platelet dysfunction. We report on a novel HPS6 homozygous frameshift variant (c.1919_1920delTC; p.Val640Glyfs*29) in a nonconsanguineous Caucasian family with two affected siblings (index patients) who presented with oculocutaneous albinism at birth and a mild bleeding phenotype during childhood and adolescence. PROCEDURE: Genetic analysis was conducted by panel-based next-generation sequencing (NGS) and Sanger sequencing...
December 4, 2016: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/27917525/a-comparison-study-of-multivariate-fixed-models-and-gene-association-with-multiple-traits-gamut-for-next-generation-sequencing
#17
Chi-Yang Chiu, Jeesun Jung, Yifan Wang, Daniel E Weeks, Alexander F Wilson, Joan E Bailey-Wilson, Christopher I Amos, James L Mills, Michael Boehnke, Momiao Xiong, Ruzong Fan
In this paper, extensive simulations are performed to compare two statistical methods to analyze multiple correlated quantitative phenotypes: (1) approximate F-distributed tests of multivariate functional linear models (MFLM) and additive models of multivariate analysis of variance (MANOVA), and (2) Gene Association with Multiple Traits (GAMuT) for association testing of high-dimensional genotype data. It is shown that approximate F-distributed tests of MFLM and MANOVA have higher power and are more appropriate for major gene association analysis (i...
December 5, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/27917031/a-new-perspective-on-sustainable-soil-remediation-case-study-suggests-novel-fungal-genera-could-facilitate-in-situ-biodegradation-of-hazardous-contaminants
#18
L M Czaplicki, E Cooper, P L Ferguson, H M Stapleton, R Vilgalys, C K Gunsch
Deciding upon a cost effective and sustainable method to address soil pollution is a challenge for many remedial project managers. High pressure to quickly achieve cleanup goals pushes for energy-intensive remedies that rapidly address the contaminants of concern with established technologies, often leaving little room for research and development especially for slower treatment technologies, such as bioremediation, for the more heavily polluted sites. In the present case study, new genomic approaches have been leveraged to assess fungal biostimulation potential in soils polluted with particularly persistent hydrophobic contaminants...
2016: Remediation (N Y)
https://www.readbyqxmd.com/read/27915479/trends-in-next-generation-sequencing-and-a-new-era-for-whole-genome-sequencing
#19
REVIEW
Sang Tae Park, Jayoung Kim
This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields...
November 2016: International Neurourology Journal
https://www.readbyqxmd.com/read/27914918/epigenetic-game-theory-how-to-compute-the-epigenetic-control-of-maternal-to-zygotic-transition
#20
REVIEW
Qian Wang, Kirk Gosik, Sujuan Xing, Libo Jiang, Lidan Sun, Vernon M Chinchilli, Rongling Wu
Epigenetic reprogramming is thought to play a critical role in maintaining the normal development of embryos. How the methylation state of paternal and maternal genomes regulates embryogenesis depends on the interaction and coordination of the gametes of two sexes. While there is abundant research in exploring the epigenetic interactions of sperms and oocytes, a knowledge gap exists in the mechanistic quantitation of these interactions and their impact on embryo development. This review aims at formulating a modeling framework to address this gap through the integration and synthesis of evolutionary game theory and the latest discoveries of the epigenetic control of embryo development by next-generation sequencing...
November 9, 2016: Physics of Life Reviews
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